In analytical systems, the ability to increase the number of analyses being carried out at any given time by a given system has been a key component to increasing the utility and extending the lifespan of such systems. In particular, by increasing the multiplex factor of analyses with a given system, one can increase the overall throughput of the system, thereby increasing its usefulness while decreasing the costs associated with that use.
Nucleic acid sequencing, in particular, DNA sequencing is an important analytical technique critical to generating genetic information from biological organisms. The increasing availability of rapid and accurate DNA sequencing methods has made possible the determination of the DNA sequences of entire genomes, including the human genome. DNA sequencing has revolutionized the field of molecular biological research. In addition, DNA sequencing has become an important diagnostic tool in the clinic, where the rapid detection of a single DNA base change or a few base changes can be used to detect for example, a genetic disease or cancer.
In optical analyses, increasing multiplex often poses increased difficulties, as it may require more complex optical systems, increased illumination or detection capabilities, and new reaction containment strategies. In some cases, systems seek to increase multiplex by many fold, and even orders of magnitude, which further implicate these considerations. Likewise, in certain cases, the analytical environment for which the systems are to be used is so highly sensitive that variations among different analyses in a given system may not be tolerable. In some cases, it is desirable for the multiplexed systems to be compact in order to effectively utilize the light that is available from the analytical reaction and to be cost effective. In addition, it is desirable that the compact systems provide high tolerance to vibration, temperature uniformity, and reasonable instrument size and weight. It would therefore be desirable to provide analytical systems that have high multiplex for their desired analysis, and particularly for use in highly sensitive reaction analyses, and in many cases, to do so while providing a compact optical system that effectively mates an array of analytical reactions with an optical detector. The present invention meets these and a variety of other needs.